Fernandes was seen sporting a protective boot after the penalty shootout victory over Brighton on Sunday in the FA Cup semi-final.
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The Portugal international played for 101 minutes before Wout Weghorst came on to replace him ahead of the shootout, raising eyebrows as United's designated penalty taker.
And with the Red Devils set to face Tottenham in a crucial top-four clash on Thursday evening, live and exclusive on talkSPORT, there were fears that the 28-year-old could miss out.
But Ten Hag has quelled those worries by insisting that Fernandes was merely wearing the protective boot as a means of injury prevention.
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He said: "It is more often that the players be protected through prevention but that has to settle down.
"So we have all seen, he played the full game and [the injury] happened in the first-half.
"But Thursday, tomorrow, is quick but we have to see coming out what is possible."
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Meanwhile, defenders Raphael Varane and Lisandro Martinez remain out of action and face a lenghty spell on the sidelines.
"There are some players who are unavailable," said Ten Hag.
"Lisandro Martinez and Raphael Varane. We have to see how Bruno Fernandes is, because we don't know yet.
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"It's a question mark. But I think, for the rest, we are quite okay."
Tottenham are in desperate need of a win after a 6-1 thrashing at the hands of Newcastle on Sunday, which saw Cristian Stellini sacked as interim manager.
Ryan Mason has taken charge until the end of the season and Ten Hag believes there will be a huge reaction from the Spurs squad.
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"It was not so often that we had to bounce back," the Dutchman said.
"It happens with all the great teams, even Real Madrid, eh? It's obvious they had a really bad defeat, of course, and that they are mad, so that can be fuel for bouncing back.
"But it's about us. An opponent can never be more hungry than us. That's how we have to prepare for the game and make sure we go on the front foot, be dominant and dictate the game."